SEED Viewer Manual/Evidence - Revision history

DanielaBartels: /* Similarities */

2008-12-08T13:31:22Z

Similarities

DanielaBartels: /* Similarities */

2008-12-08T13:30:31Z

Similarities

DanielaBartels: /* Visual Protein Evidence */

2008-12-08T11:51:33Z

Visual Protein Evidence

DanielaBartels: /* Functionally Coupled */

2008-12-05T09:52:35Z

Functionally Coupled

DanielaBartels: /* Similarities */

2008-12-05T09:52:05Z

Similarities

TobiasPaczian: /* Similarities */

2008-11-25T14:08:11Z

Similarities

TobiasPaczian: /* Similarities */

2008-11-25T13:59:49Z

Similarities

TobiasPaczian: /* Similarities */

2008-11-25T13:58:44Z

Similarities

TobiasPaczian: /* Similarities */

2008-11-25T13:57:21Z

Similarities

TobiasPaczian: /* Domains */

2008-11-25T13:56:40Z

Domains

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 [[Image:EvidenceSims2.png]]
-You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.
+You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect|List Select]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.
 [[Image:EvidenceFilter.png]]

@@ Line 63: / Line 63: @@
 [[Image:EvidenceSims2.png]]
-You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.
+You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.
 [[Image:EvidenceFilter.png]]

@@ Line 5: / Line 5: @@
 == Visual Protein Evidence ==
-After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.
+After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.
 === Location ===

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 === Functionally Coupled ===
-This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.
+This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.
 [[Image:EvidenceFCs.png]]

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 === Similarities ===
-The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at  [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.
+The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at  [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.
 The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

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 The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.
-If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.
+If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.
 [[Image:EvidenceSims1.png]]

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 This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.
-Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature.
+Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.
 The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

@@ Line 15: / Line 15: @@
 === Domains ===
-This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).
+This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).
 Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.